Error with make on cluster (QT issues)

[Peter Patalano]

I am trying to compile from source on a cluster and am having issues when I make. I have tried to use a prebuilt version and am still having issues. When I use the qt external which comes wiht SimVascular I get this error

Code: Select all

[ 57%] Linking CXX shared library ../../../../lib/plugins/liborg_sv_gui_qt_projectmanager.so
[ 57%] Built target org_sv_gui_qt_projectmanager
[ 57%] Generating moc_sv4gui_PathPlanningPluginActivator.cpp
[ 58%] Generating ui_sv4gui_PathCreate.h
/home/pp872/SimVascularSrc/Build/Externals-build/svExternals/bin/qt-5.4.2/bin/uic: error while loading shared libraries: libicui18n.so.42: cannot open shared object file: No such file or directory
make[5]: *** [Source/sv4gui/Plugins/org.sv.gui.qt.pathplanning/ui_sv4gui_PathCreate.h] Error 127
make[4]: *** [Source/sv4gui/Plugins/org.sv.gui.qt.pathplanning/CMakeFiles/org_sv_gui_qt_pathplanning.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [SimVascular-prefix/src/SimVascular-stamp/SimVascular-build] Error 2
make[1]: *** [CMakeFiles/SimVascular.dir/all] Error 2
make: *** [all] Error 2 

Any help is appreciated

[Justin Tran]

Hi Peter,

Thank you for your question and interest in SimVascular! Just a clarifying question: are you planning on using the SimVascular front-end GUI on the cluster? Or do you just plan to run flow simulations on it? It is quite common for users to do the model construction and meshing in the front-end GUI using the pre-built versions on their desktop machines, then using the cluster to run the flow simulations.

I ask this because it is much easier to compile the flow solver on clusters than it is to compile the entire front-end GUI on clusters (since the GUI uses lots of packages like QT that may not be standard on Linux computing clusters). The Github link to JUST the solver source files is here: https://github.com/SimVascular/svSolver, and instructions on how to compile are given below:

1. First, make sure you load appropriate compilers. We recommend gcc/gfortran compilers and the OpenMPI implementation of the MPI standard. Intel compilers and MPICH is also possible. If your cluster uses a module-based way of organizing software libraries, you will have to use commands like:

module load gcc
module load openmpi

2. Clone the code repository into your cluster: git clone https://github.com/SimVascular/svSolver.git svsolver
3. Move into the build folder: cd svsolver/BuildWithMake
4. Download VTK binaries: ./get-vtk-binaries.sh centos_6
5. Set parameters for cluster installation: cp SampleOverrides/centos_6/global_overrides.mk . (<---- notice period!)
5a. Open the global_overrides.mk in a text editor (i.e. vim or emacs) and edit your MPI choice. The default is "NOMPI", but you can change the flag according to the MPI implementation you have (OpenMPI or MPICH).
6. Compile the code: make

Hope this helps! Let us know if you are able to compile the flow solver on the cluster.

[Peter Patalano]

Thanks for the prompt response. Was not planning to run the GUI on the cluster. I just wasn't clear about the documentation for the solver alone. I will use your instructions once I get to a computer and keep this thread updated. Thanks again.

[Peter Patalano]

It compiled. Thanks so much for your help.

[Peter Patalano]

Actually it did not compile properly, the only binaries I end up with are .exe and include svpost.exe, svpost-gcc-gfortran.exe, svpre.exe and svpre-gcc-fortran.exe.

[Justin Tran]

Can you try to recomplile it and post the error messages? It might be that you are missing some other libraries.

[Peter Patalano]

I recompiled and it worked. Not sure I did anything differently. Thanks for all your help.

[Tanmay Shidhore]

Hi Justin,

Thanks for detailing the steps to build svsolver; I was able to replicate them on a cluster running centOS without any issues. However, when I tried to build svsolver on an ubuntu 18.04 machine using the same steps, it gave me the following error while running make:

relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC

This error message was referencing some of the pre-built vtk binaries I had downloaded so does it have something to do with the way these binaries were compiled originally? Thanks.

[David Parker]

Hi Tanmay,

For Ubuntu 18 you can use the svSolver installer.

Cheers,
Dave

[Tanmay Shidhore]

Hi David,

Since I don't have admin access on this machine, I thought that the installer might not work in my case. Is there a way I can use the installer as a user? Thanks